diff options
Diffstat (limited to 'lib/validation_db.rb')
| -rwxr-xr-x[-rw-r--r--] | lib/validation_db.rb | 154 |
1 files changed, 132 insertions, 22 deletions
diff --git a/lib/validation_db.rb b/lib/validation_db.rb index 1152abf..0d5db21 100644..100755 --- a/lib/validation_db.rb +++ b/lib/validation_db.rb @@ -4,21 +4,10 @@ #end require "lib/merge.rb" -unless ActiveRecord::Base.connected? - ActiveRecord::Base.establish_connection( - :adapter => @@config[:database][:adapter], - :host => @@config[:database][:host], - :database => @@config[:database][:database], - :username => @@config[:database][:username], - :password => @@config[:database][:password] - ) - ActiveRecord::Base.logger = Logger.new("/dev/null") -end - module Lib - VAL_PROPS_GENERAL = [ :validation_uri, :model_uri, :algorithm_uri, :training_dataset_uri, :prediction_feature, - :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri, :created_at ] + VAL_PROPS_GENERAL = [ :validation_uri, :validation_type, :model_uri, :algorithm_uri, :training_dataset_uri, :prediction_feature, + :test_dataset_uri, :test_target_dataset_uri, :prediction_dataset_uri, :date ] VAL_PROPS_SUM = [ :num_instances, :num_without_class, :num_unpredicted ] VAL_PROPS_AVG = [:real_runtime, :percent_without_class, :percent_unpredicted ] VAL_PROPS = VAL_PROPS_GENERAL + VAL_PROPS_SUM + VAL_PROPS_AVG @@ -28,7 +17,8 @@ module Lib # :classification_statistics VAL_CLASS_PROPS_SINGLE_SUM = [ :num_correct, :num_incorrect, :confusion_matrix ] - VAL_CLASS_PROPS_SINGLE_AVG = [ :percent_correct, :percent_incorrect, :weighted_area_under_roc ] + VAL_CLASS_PROPS_SINGLE_AVG = [ :percent_correct, :percent_incorrect, + :weighted_area_under_roc, :accuracy, :weighted_accuracy ] VAL_CLASS_PROPS_SINGLE = VAL_CLASS_PROPS_SINGLE_SUM + VAL_CLASS_PROPS_SINGLE_AVG # :class_value_statistics @@ -43,26 +33,146 @@ module Lib :true_negative_rate, :true_positive_rate ] #:precision, :recall, VAL_CLASS_PROPS = VAL_CLASS_PROPS_SINGLE + VAL_CLASS_PROPS_PER_CLASS - VAL_CLASS_PROPS_EXTENDED = VAL_CLASS_PROPS + [:accuracy] # :regression_statistics VAL_REGR_PROPS = [ :root_mean_squared_error, :mean_absolute_error, :r_square, :target_variance_actual, :target_variance_predicted, :sum_squared_error, :sample_correlation_coefficient ] CROSS_VAL_PROPS = [:dataset_uri, :num_folds, :stratified, :random_seed] - CROSS_VAL_PROPS_REDUNDANT = [:crossvalidation_uri, :algorithm_uri, :created_at] + CROSS_VAL_PROPS + CROSS_VAL_PROPS_REDUNDANT = [:crossvalidation_uri, :algorithm_uri, :date] + CROSS_VAL_PROPS - ALL_PROPS = VAL_PROPS + VAL_CV_PROPS + VAL_CLASS_PROPS_EXTENDED + VAL_REGR_PROPS + CROSS_VAL_PROPS + ALL_PROPS = VAL_PROPS + VAL_CV_PROPS + VAL_CLASS_PROPS + VAL_REGR_PROPS + CROSS_VAL_PROPS VAL_MERGE_GENERAL = VAL_PROPS_GENERAL + VAL_CV_PROPS + [:classification_statistics, :regression_statistics] + CROSS_VAL_PROPS VAL_MERGE_SUM = VAL_PROPS_SUM + VAL_CLASS_PROPS_SINGLE_SUM + VAL_CLASS_PROPS_PER_CLASS_SUM VAL_MERGE_AVG = VAL_PROPS_AVG + VAL_CLASS_PROPS_SINGLE_AVG + VAL_CLASS_PROPS_PER_CLASS_AVG + VAL_REGR_PROPS - - class Validation < ActiveRecord::Base - serialize :classification_statistics - serialize :regression_statistics + + +# class Validation < ActiveRecord::Base +# serialize :classification_statistics +# serialize :regression_statistics +# +# alias_attribute :date, :created_at + + class Validation + include DataMapper::Resource + + property :id, Serial + property :validation_type, String, :length => 512 + property :model_uri, String, :length => 512 + property :algorithm_uri, String, :length => 512 + property :training_dataset_uri, String, :length => 512 + property :test_target_dataset_uri, String, :length => 512 + property :test_dataset_uri, String, :length => 512 + property :prediction_dataset_uri, String, :length => 512 + property :prediction_feature, String, :length => 512 + property :created_at, DateTime + property :num_instances, Integer + property :num_without_class, Integer + property :num_unpredicted, Integer + property :crossvalidation_id, Integer + property :crossvalidation_fold, Integer + property :real_runtime, Float + property :percent_without_class, Float + property :percent_unpredicted, Float + property :classification_statistics, Object + property :regression_statistics, Object + property :finished, Boolean, :default => false + + attr_accessor :subjectid + + after :save, :check_policy + private + def check_policy + OpenTox::Authorization.check_policy(validation_uri, subjectid) + end + + public + def date + created_at + end + + def validation_uri + raise "no id" if self.id==nil + $url_provider.url_for("/"+self.id.to_s, :full) + end + + def crossvalidation_uri + $url_provider.url_for("/crossvalidation/"+self.crossvalidation_id.to_s, :full) if self.crossvalidation_id + end + + def self.classification_property?( property ) + VAL_CLASS_PROPS.include?( property ) + end + + def self.depends_on_class_value?( property ) + VAL_CLASS_PROPS_PER_CLASS.include?( property ) + end + + def self.complement_exists?( property ) + VAL_CLASS_PROPS_PER_CLASS_COMPLEMENT_EXISTS.include?( property ) + end + end - class Crossvalidation < ActiveRecord::Base +# class Crossvalidation < ActiveRecord::Base +# alias_attribute :date, :created_at + class Crossvalidation + include DataMapper::Resource + + property :id, Serial + property :algorithm_uri, String, :length => 512 + property :dataset_uri, String, :length => 512 + property :created_at, DateTime + property :num_folds, Integer, :default => 10 + property :random_seed, Integer, :default => 1 + property :finished, Boolean, :default => false + property :stratified, Boolean, :default => false + + attr_accessor :subjectid + + after :save, :check_policy + private + def check_policy + OpenTox::Authorization.check_policy(crossvalidation_uri, subjectid) + end + + public + def date + created_at + end + + def crossvalidation_uri + raise "no id" if self.id==nil + $url_provider.url_for("/crossvalidation/"+self.id.to_s, :full) if self.id + end + + # convenience method to list all crossvalidations that are unique + # in terms of dataset_uri,num_folds,stratified,random_seed + # further conditions can be specified in __conditions__ + def self.find_all_uniq(conditions={}, subjectid=nil ) + #cvs = Lib::Crossvalidation.find(:all, :conditions => conditions) + cvs = Lib::Crossvalidation.all(:conditions => conditions) + uniq = [] + cvs.each do |cv| + next if AA_SERVER and !OpenTox::Authorization.authorized?(cv.crossvalidation_uri,"GET",subjectid) + match = false + uniq.each do |cv2| + if cv.dataset_uri == cv2.dataset_uri and cv.num_folds == cv2.num_folds and + cv.stratified == cv2.stratified and cv.random_seed == cv2.random_seed + match = true + break + end + end + uniq << cv unless match + end + uniq + end end end + + +Lib::Validation.auto_upgrade! +Lib::Validation.raise_on_save_failure = true +Lib::Crossvalidation.auto_upgrade! +Lib::Crossvalidation.raise_on_save_failure = true |